Google has recently announced a new guideline for Webmaster Tools that specifically notes that all users should allow Googlebot access to crawl all CSS and Javascript files; preventing Googlebot from doing such may result in a negative impact on your overall ranking. So, why shouldn’t we block these files? The main reason is because doing so can inhibit all of your valuable content from being found and properly indexed by Google’s algorithms. Everything on any given webpage should be detectable; Google wants to see the HTML of a page and any other assets, specifically images, CSS or Javascript files.
See more information here on Google’s blog and make sure that you are using the correct settings and strategies for ideal indexing.